Can't use pen to navigate in viewport
the emulate middle-mouse button does not directly navigate for you when you use the pen, rather it adds a key or keys that in combination with the pen touching and moving navigate like with the mouse.

In that regard, once activated, the Alt button held down will be used to rotate with the pen like you would with the MMB.

If you use Alt+Shift, you can pan the screen like you would with Shift+MMB.

And using Alt+Ctrl gives your pen the zoom based on moving up or down movement like you would normally do with Ctrl+MMB.

As you can see, the emulation essentially replaces the MMB with the Alt key. So some other functions like loop select that would normally use Alt+LMB, will have other keys like a double LMB(click).

Happy Blending.